# SET INPUT AND OUTPUT PATH
# Using function here() wil provide path to the OCR_Pipeline(package) folder on your computer,
# the input and output separate folers are in "/OCR_Pipeline/Data".
# Recomend to move the result to different folder before every analysis.
#
# To choose different folder in your coputer as I/O folder write entire Path to the folder.
INPUT_PATH <- here('/Data/INPUT')
OUTPUT_PATH <- here('/Data/OUTPUT')
Removed outliars in each iteration:
## 1 Well outliares: 788 -- 11.52047 %
## 2 Well outliares: 296 -- 4.327485 %
## 3 Well outliares: 33 -- 0.4824561 %
## 4 Well outliares: 0 -- 0 %
## 1 Point outliares: 158 -- 2.839684 %
## 2 Point outliares: 58 -- 1.042416 %
## 3 Point outliares: 30 -- 0.5391804 %
## 4 Point outliares: 17 -- 0.3055356 %
## 5 Point outliares: 4 -- 0.07189073 %
## 6 Point outliares: 1 -- 0.01797268 %
## 7 Point outliares: 1 -- 0.01797268 %
## 8 Point outliares: 0 -- 0 %
## Tolat well outliars: 16.71905 %
## Tolat single point outliars: 4.026343 %
TO DO: convert graph to aditive add legends
OCR only intervals 1 to 4
| Int1 | Int2 | Int3 | Int4 | Sample | norm.Int1 | norm.Int2 | norm.Int3 | norm.Int4 |
|---|---|---|---|---|---|---|---|---|
| 4.103 | 3.136 | 4.959 | 2.870 | 24-post-0 | 60.503 | 23.022 | 142.478 | 17.633 |
| 2.908 | 1.809 | 3.407 | 1.670 | 24-pre-1 | 18.325 | 6.104 | 30.186 | 5.311 |
| 4.080 | 3.087 | 5.162 | 2.962 | 31 post-2 | 59.174 | 21.902 | 174.572 | 19.341 |
| 4.822 | 3.863 | 6.185 | 3.638 | 42 pre-2 | 124.157 | 47.601 | 485.624 | 38.024 |
| 3.504 | 2.557 | 4.414 | 2.333 | 33-pre-3 | 33.257 | 12.894 | 82.559 | 10.313 |
| 3.941 | 2.905 | 4.831 | 2.869 | 34-post-4 | 51.466 | 18.267 | 125.330 | 17.618 |
| 3.388 | 2.460 | 3.982 | 2.051 | 34-pre-5 | 29.606 | 11.702 | 53.603 | 7.779 |
| 3.696 | 2.920 | 4.643 | 2.745 | S-36pre-6 | 40.266 | 18.539 | 103.828 | 15.569 |
| 3.643 | 2.801 | 4.546 | 2.663 | S-43pre-6 | 38.194 | 16.458 | 94.262 | 14.335 |
| 3.609 | 2.682 | 4.400 | 2.481 | 36-pre-7 | 36.924 | 14.616 | 81.438 | 11.950 |
| 3.594 | 2.472 | 4.677 | 2.363 | 39-post-8 | 36.378 | 11.844 | 107.475 | 10.622 |
| 3.586 | 2.409 | 4.564 | 2.428 | 39-pre-9 | 36.084 | 11.123 | 95.934 | 11.334 |
| 2.993 | 1.586 | 3.949 | 1.559 | 42 post-10 | 19.948 | 4.884 | 51.885 | 4.756 |
| 3.403 | 1.894 | 3.931 | 1.891 | #46 pre-10 | 30.043 | 6.645 | 50.977 | 6.629 |
| 3.845 | 2.889 | 4.616 | 2.800 | 43 post-11 | 46.750 | 17.981 | 101.051 | 16.438 |
| 3.756 | 2.930 | 4.437 | 2.763 | 49 pre-11 | 42.772 | 18.719 | 84.496 | 15.846 |
| 3.979 | 2.946 | 4.883 | 2.708 | 46 post-12 | 53.439 | 19.028 | 131.984 | 15.001 |
| 3.792 | 2.688 | 4.792 | 2.331 | 40 pre-12 | 44.353 | 14.700 | 120.512 | 10.291 |
| 3.555 | 2.754 | 4.378 | 2.942 | 49-post-13 | 34.981 | 15.712 | 79.673 | 18.958 |
| Int1 | Int2 | Int3 | Int4 | Sample |
|---|---|---|---|---|
| 0.013 | 0.016 | 0.020 | 0.015 | 24-post-0 |
| 0.026 | 0.032 | 0.043 | 0.032 | 24-pre-1 |
| 0.009 | 0.012 | 0.016 | 0.012 | 31 post-2 |
| 0.011 | 0.015 | 0.018 | 0.013 | 42 pre-2 |
| 0.013 | 0.018 | 0.021 | 0.017 | 33-pre-3 |
| 0.016 | 0.020 | 0.031 | 0.019 | 34-post-4 |
| 0.039 | 0.049 | 0.063 | 0.048 | 34-pre-5 |
| 0.017 | 0.022 | 0.026 | 0.020 | S-36pre-6 |
| 0.024 | 0.029 | 0.040 | 0.029 | S-43pre-6 |
| 0.014 | 0.017 | 0.022 | 0.016 | 36-pre-7 |
| 0.031 | 0.036 | 0.045 | 0.037 | 39-post-8 |
| 0.016 | 0.020 | 0.028 | 0.020 | 39-pre-9 |
| 0.042 | 0.060 | 0.071 | 0.061 | 42 post-10 |
| 0.038 | 0.052 | 0.059 | 0.046 | #46 pre-10 |
| 0.014 | 0.018 | 0.024 | 0.017 | 43 post-11 |
| 0.013 | 0.015 | 0.022 | 0.015 | 49 pre-11 |
| 0.021 | 0.026 | 0.031 | 0.025 | 46 post-12 |
| 0.018 | 0.022 | 0.029 | 0.022 | 40 pre-12 |
| 0.016 | 0.022 | 0.026 | 0.019 | 49-post-13 |
## Using Sample as id variables
## Using Sample as id variables
## Using Sample as id variables
Remove outliars
## 1 Well outliares: 339 -- 7.080201 %
## 2 Well outliares: 107 -- 2.234754 %
## 3 Well outliares: 93 -- 1.942356 %
## 4 Well outliares: 49 -- 1.023392 %
## 5 Well outliares: 49 -- 1.023392 %
## 6 Well outliares: 12 -- 0.2506266 %
## 7 Well outliares: 0 -- 0 %
## 1 Point outliares: 104 -- 2.567901 %
## 2 Point outliares: 19 -- 0.4691358 %
## 3 Point outliares: 10 -- 0.2469136 %
## 4 Point outliares: 0 -- 0 %
## Tolat well outliars: 13.81145 %
## Tolat single point outliars: 2.830389 %
for (smpl in unique(dr_ecar$sample_id)) {
plot <- ggplot(filter(dr_ecar, sample_id == smpl), aes(Measurement, LECAR))+
ggtitle(paste0("SAMPLE: ", smpl))+
geom_line(aes(group = Well),size = 0.2, color = "grey") +
geom_point(aes(Measurement, LECAR, color = out))+
xlab("Interval")#+
#facet_grid(Protocol ~ . )
print(plot +theme_bw())
}
Make clear separation of those two ECAR vs OCR # Estimates and bionergetics
| Int1 | Int2 | Int5 | Sample | norm.Int1 | norm.Int2 | norm.Int5 |
|---|---|---|---|---|---|---|
| 3.805 | 4.216 | 3.051 | 24-post-0 | 44.931 | 67.744 | 21.129 |
| 3.098 | 3.333 | 2.267 | 24-pre-1 | 22.153 | 28.011 | 9.651 |
| 3.486 | 3.890 | 2.854 | 31 post-2 | 32.660 | 48.893 | 17.360 |
| 3.884 | 4.408 | 3.435 | 42 pre-2 | 48.606 | 82.102 | 31.033 |
| 3.285 | 3.654 | 2.600 | 33-pre-3 | 26.709 | 38.630 | 13.461 |
| 3.443 | 3.996 | 2.870 | 34-post-4 | 31.265 | 54.388 | 17.645 |
| 3.206 | 3.622 | 2.568 | 34-pre-5 | 24.676 | 37.410 | 13.044 |
| 3.182 | 3.543 | 2.543 | S-36pre-6 | 24.083 | 34.578 | 12.718 |
| 3.330 | 3.782 | 2.734 | S-43pre-6 | 27.945 | 43.898 | 15.395 |
| 3.401 | 3.673 | 2.489 | 36-pre-7 | 29.993 | 39.375 | 12.049 |
| 3.644 | 3.939 | 2.802 | 39-post-8 | 38.261 | 51.386 | 16.484 |
| 3.621 | 3.897 | 2.786 | 39-pre-9 | 37.384 | 49.273 | 16.217 |
| 3.240 | 3.440 | 2.464 | 42 post-10 | 25.541 | 31.193 | 11.754 |
| 3.603 | 3.967 | 2.786 | #46 pre-10 | 36.695 | 52.837 | 16.213 |
| 3.258 | 3.746 | 2.626 | 43 post-11 | 26.001 | 42.334 | 13.814 |
| 3.210 | 3.620 | 2.430 | 49 pre-11 | 24.790 | 37.344 | 11.364 |
| 3.480 | 4.160 | 2.995 | 46 post-12 | 32.451 | 64.071 | 19.989 |
| 3.123 | 3.820 | 2.927 | 40 pre-12 | 22.703 | 45.614 | 18.665 |
| 3.219 | 3.509 | 2.241 | 49-post-13 | 25.003 | 33.432 | 9.403 |
| Int1 | Int2 | Int5 | Sample |
|---|---|---|---|
| 0.008 | 0.011 | 0.018 | 24-post-0 |
| 0.007 | 0.009 | 0.015 | 24-pre-1 |
| 0.009 | 0.012 | 0.020 | 31 post-2 |
| 0.009 | 0.011 | 0.018 | 42 pre-2 |
| 0.007 | 0.010 | 0.014 | 33-pre-3 |
| 0.012 | 0.017 | 0.028 | 34-post-4 |
| 0.007 | 0.010 | 0.015 | 34-pre-5 |
| 0.010 | 0.013 | 0.023 | S-36pre-6 |
| 0.010 | 0.012 | 0.020 | S-43pre-6 |
| 0.008 | 0.010 | 0.016 | 36-pre-7 |
| 0.010 | 0.012 | 0.019 | 39-post-8 |
| 0.007 | 0.009 | 0.015 | 39-pre-9 |
| 0.010 | 0.015 | 0.025 | 42 post-10 |
| 0.008 | 0.011 | 0.023 | #46 pre-10 |
| 0.008 | 0.011 | 0.017 | 43 post-11 |
| 0.008 | 0.010 | 0.020 | 49 pre-11 |
| 0.009 | 0.012 | 0.020 | 46 post-12 |
| 0.009 | 0.011 | 0.019 | 40 pre-12 |
| 0.009 | 0.011 | 0.021 | 49-post-13 |
## Using Sample as id variables
## Using Sample as id variables
## Using Sample as id variables